OTU clustering

The OTU clustering tool clusters a collection of reads to operational taxonomy units.

To run the tool, go to

Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Metagenomics (Image wma_folder_open_flat_16_n_p) | Amplicon-based OTU clustering (Image otutools_open_16_n_p) | OTU clustering (Image OTU_clustering_16_n_p).

The tool aligns the reads to all OTUs to create an "alignment score" for each OTU. If a read cannot be put into an already existing OTU (because there is no single OTU that is similar enough, i.e., within 97% similarity), the algorithm tries to optimize the alignment score by allowing to "cross over" from one database reference to another at a cost (the chimera crossover cost). To speed up the chimera crossover detection algorithm, the read is not aligned to all OTUs but only to some "promising candidates" found via a k-mer search. If the best match that can be constructed has at least one crossover and the "constructed alignment" is at least as good as the "similarity percentage", then the read is being considered chimeric.

By default, the similarity percentage parameter is set to 97% in the OTU Clustering tool. Therefore without the chimera crossover cost, the constructed alignments difference score can only be 3% at most. The smaller the chimeric cost, the more likely it is that a read is deemed chimeric; setting it too high decreases the chimeric detection.

The OTU clustering tool produces several outputs:



Subsections